diff options
Diffstat (limited to 'sci-biology')
33 files changed, 428 insertions, 385 deletions
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz Binary files differindex 6530d34211fd..ab77a5ae6d14 100644 --- a/sci-biology/Manifest.gz +++ b/sci-biology/Manifest.gz diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest index 49f0d85cb203..dab34c2f1993 100644 --- a/sci-biology/allpathslg/Manifest +++ b/sci-biology/allpathslg/Manifest @@ -1,4 +1,5 @@ +AUX allpathslg-52488-gcc7.patch 790 BLAKE2B d3993e840b7b53791b0830fc993553c45c00d5d81881750066327106ad45f13bd0f4dba48c8cc0bdf3655d20ff3cefa659b8d41f582a73376188109860e5f2eb SHA512 bde085541f74278aba8edd1c41dd3a2541a7ce7f3a6647b5f3ed19613545bbfff287463e90e785b4476c677d2456d4c87818730b95941b27744549fcdd62d935 DIST allpathslg-52488-patchset.tar.bz2 11405 BLAKE2B 7a4c36884ac95a4eb23291720e422ce1ec41d0bea3a0b10582aa1d8154234971eb8d06979a969e65c1ec1eab031d2500a1ec40809019c8b4aa1d1d2e81427dbe SHA512 a1d58c131afeef04a9d7a2520fcd28a853317323fdcab1a253cb2548546bbc559993c74a68a8032a5d0e865ac2c2d53ff6b4c149aade2d1f87a2ab4116ebe4cc DIST allpathslg-52488.tar.gz 3121949 BLAKE2B b75904f9e8256a14c97abae45a0cb41718f95d27a4a072b6144bd125abb57682faa180de6a18399ab4fa43988344c436ca1eab8412433353fcc746c432c33031 SHA512 c44ef1a3ed5b343bf096663309cc399e79d65e83175232743cf330fd0d426633bd0d388922fd0c73ac0927d85ea9005549c8e4f7711c79fea7107068510ef30d -EBUILD allpathslg-52488-r2.ebuild 1547 BLAKE2B 0ff97cce907b769446002e704f04524450e5370aba0a5f5fcf66313851fa3708e4c204e1dcde637537ebffaa1baf549b7aa1bc097bc293ee9d43488aa952f205 SHA512 39958550cd4ba2d2e17843860a0354f383fe15850b393aa8a48edc76e59307899afedc878ea68f8c2077f720d6e6f631d32ca1b1c11256e5800cb40d6b9027a6 +EBUILD allpathslg-52488-r2.ebuild 1016 BLAKE2B e707f2cebafd829c0ccf712a5b72eb10c39663ccfa3f2a8f279200286f609905b3be756d64c42748667e4171aef36435bb9386f8d807db29584bdc74ceee92ab SHA512 106002b58ebd2616d216e61d164102f5eed7204a19d470a30d2f0e6ef685009fa737866c563fccc1980a6577b1f2e30af01756f291701914a67101a96a60bd87 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild index e68430e2462d..964904d66551 100644 --- a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild +++ b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild @@ -23,31 +23,17 @@ DEPEND=" dev-libs/boost:=" PATCHES=( - "${WORKDIR}/${P}-patchset/${P}_fix-buildsystem.patch" - "${WORKDIR}/${P}-patchset/${P}_remove-namespace-std.patch" + "${WORKDIR}"/${P}-patchset/${P}_fix-buildsystem.patch + "${WORKDIR}"/${P}-patchset/${P}_remove-namespace-std.patch + "${FILESDIR}"/${P}-gcc7.patch ) pkg_pretend() { - # as of release 44849, GCC 4.7.0 (or higher) is required - # seems pre gcc-4.7 users must stay with: - # ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-01/allpathslg-44837.tar.gz - if [[ ${MERGE_TYPE} != binary ]]; then - tc-is-gcc && [[ $(gcc-version) < 4.7 ]] && \ - die "You need to use gcc >4.7" - fi + [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp } pkg_setup() { - if ! tc-has-openmp; then - ewarn "OpenMP is not available in your current selected compiler" - - if tc-is-clang; then - ewarn "OpenMP support in sys-devel/clang is provided by sys-libs/libomp," - ewarn "which you will need to build ${CATEGORY}/${PN} with USE=\"openmp\"" - fi - - die "need openmp capable compiler" - fi + [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp } src_prepare() { diff --git a/sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch b/sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch new file mode 100644 index 000000000000..7c5e1267e4e9 --- /dev/null +++ b/sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch @@ -0,0 +1,13 @@ +--- a/src/paths/long/VariantCallTools.cc ++++ b/src/paths/long/VariantCallTools.cc +@@ -1870,8 +1870,8 @@ + bool i_is_indel = (change[i].first.size() != change[i].second.size()); + if (i_is_indel) inserted_base += change[i].second.size()-1; + size_t j = i + 1; +- while (j < edits.size() && abs(edits[j].second - edits[j-1].second +- - change[j-1].first.size()) < MinClumpSep) { ++ while (j < edits.size() && std::abs(edits[j].second - edits[j-1].second ++ - static_cast<int>(change[j-1].first.size())) < MinClumpSep) { + nmatch += edits[j].second - edits[j-1].second - change[j-1].first.size(); + bool j_is_indel = (change[j].first.size() != change[j].second.size()); + if (j_is_indel) diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest index c72595263210..bbf916477036 100644 --- a/sci-biology/bowtie/Manifest +++ b/sci-biology/bowtie/Manifest @@ -8,10 +8,7 @@ AUX bowtie-1.1.2-tbb-tinythread-missing.patch 554 BLAKE2B 745629aa93f2e74191b944 AUX bowtie-1.1.2-unbundle-seqan.patch 751 BLAKE2B d9689b298f21f4619dbbed96b58d8ae7fc5f646539ae33291222d282153b545ad6fb3e30fe1ba5f0f452e2f3e7e9706b6761f5d4184dcd5ad96a55ccc7b246be SHA512 9a68ccc98774a2c9ddb8f45b5ed009230d14d3e29837c6dd8aac34e298f57208361ef45d0e7d9d074495f3465b58f08606cced9e4fccb549785591ff954cb2b8 AUX bowtie-2.2.9-fix-c++14.patch 687 BLAKE2B a75f473f429379789a97142d7820fb19fc1a64b764236c6fa1c068cefb03e37a58b41b0a515a62d42e85b3131f0dfe8f2bb856126528099277394674a0e53248 SHA512 3aa6e7a30fdf93ae564091ce9b87338ab9feccbd0c873f4130af71dc94fd3b27527b42a93f13471a2613bad44dbacd639d17515000f03856695a0021ce14dfc5 DIST bowtie-1.1.2-src.zip 7713258 BLAKE2B ac10aca905099b5a70d3fab6f90e2dc4713bf7b460d027abf89a6ef6103979724e70b2915a86ffa571b59dcd9df768c80be1846cccd08f7f85dd402ce64c0cb0 SHA512 3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8 -DIST bowtie2-2.2.6-source.zip 5728779 BLAKE2B acd821376755e6bebfd58c39012a370b1aadf4cf8c52eafa1c648c93a0cab695c9c37761498260ed709bc25eb0b671797ff1c74da9787d616c8c39d1296a37eb SHA512 3ab5a5475cf214affd91e0d1782fd2d6dedccd979e3c809b5dfb272726d99ff1c7b59d92e387b187a7c2e43557786a1085186ccb96588de91212caf2eb94ce4f DIST bowtie2-2.2.9-source.zip 5734235 BLAKE2B ec48e09fe05403d1085bb4e0c6ef1325b8912da0a8c942061c34f3381c6dd7ccdcc64c4bcdbb18c1da84ac57e1e34cc866fe79809c33c2769a8d75ecde7d0846 SHA512 ead8f7641f3231638d986f9e500bc4ec7afe1e542048465bfcc2e93e2b2d2e499f0dd8aa5c1e3e21df285c9d195b187682eb7e12be4a408f6c50fb97c0e0a205 EBUILD bowtie-1.1.2-r1.ebuild 1643 BLAKE2B 81f79b8b8d9b9a56061bf92df193a21e2db03bdacb6290020e8fb2426e3e1cf9e5a6a802cb6fa5f5f68be8d7f92f749e14c0c3528ebad5825d3927bcf33ca483 SHA512 8b5c22f29aafb5977313ea002fcd654ac991015f7808f02f8e02c2105dd9a6fa77b5f5342e82d38b07674c93dbe397333be78f6d1ca9a24a60531d6a40efe382 -EBUILD bowtie-1.1.2.ebuild 1058 BLAKE2B 4aae2773c629826866242b9c62f08e904d70f55b5094b46f727ae59d0fe75845ad3c809cde724753f0ada493294340e59a2290960f6049f3795d4352b9ca4a6a SHA512 33bd306019d37f3eb05922805e7035bf82bd40c21934c541bd6c56522afc1aa2ebfa900024d72cd0555e290560de07b1adadb98673100b934f53779c2e40376f -EBUILD bowtie-2.2.6.ebuild 1230 BLAKE2B 0382c42265c5fd5192d8d177f91f803fd4f9b28f107bcffed14573386c283d59e77d6ca72872f1c86c5f8a79f05263257865a39cfac64a8d4d6c77acb2aa299b SHA512 7c1546de18fa549defa619877688e38b2e90a5875ac9d6ca2728ae7788e495870efbbafeaabe0e3a79788e393e8d273b715fd9bcfef4267ac5daba1dd18a87ff EBUILD bowtie-2.2.9.ebuild 1277 BLAKE2B b9cf9edc34af3f01eb1cde1510637bbcbaf7206d9a24135d859d14dcefe793abd0b78dd19dbcd1835840514e754061aee86a79d5992ca68d316c64c98bb4891c SHA512 40e22698d5df241b8b98c601f8ed22276d39f4c9818bb23afec0a39b625fd38a0fdb3f4b4d6f8c01b458e2b6b3464a7ee8a135bd446f3488354eeca9934daa85 MISC metadata.xml 528 BLAKE2B 310fb406a0dbe56b194ae13cf521264e105f9d849b09e10d5d7e556c7d00a9cc7a0f9546a91e43f30344c9ec14a76e0d8a3f037fb4cb91bba68999d9f45b69e0 SHA512 1eb83cbd7d7e747bc94021051ba6ae0bf22411091287b754851a9f6824b263b6ca83c9a0d055c0b6ab24963ceea9b32d76bf1b343f48a3ee4bd322fec539b301 diff --git a/sci-biology/bowtie/bowtie-1.1.2.ebuild b/sci-biology/bowtie/bowtie-1.1.2.ebuild deleted file mode 100644 index 1ada8a0fdc2b..000000000000 --- a/sci-biology/bowtie/bowtie-1.1.2.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils toolchain-funcs - -DESCRIPTION="Popular short read aligner for Next-generation sequencing data" -HOMEPAGE="http://bowtie-bio.sourceforge.net/" -SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" - -LICENSE="Artistic" -SLOT="1" -KEYWORDS="amd64 x86 ~x64-macos" - -IUSE="examples +tbb" - -DEPEND="app-arch/unzip - tbb? ( dev-cpp/tbb )" -RDEPEND="" - -DOCS=( AUTHORS NEWS TUTORIAL doc/README ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -src_prepare() { - # always include tinythread.cpp - epatch "${FILESDIR}/${P}-tbb-tinythread-missing.patch" -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS}" \ - WITH_TBB="$(usex tbb 1 0)" -} - -src_install() { - dobin ${PN} ${PN}-* - - exeinto /usr/libexec/${PN} - doexe scripts/* - - newman MANUAL ${PN}.1 - einstalldocs - - if use examples; then - insinto /usr/share/${PN} - doins -r genomes indexes - fi -} diff --git a/sci-biology/bowtie/bowtie-2.2.6.ebuild b/sci-biology/bowtie/bowtie-2.2.6.ebuild deleted file mode 100644 index 29826473a3b3..000000000000 --- a/sci-biology/bowtie/bowtie-2.2.6.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils toolchain-funcs - -DESCRIPTION="Popular short read aligner for Next-generation sequencing data" -HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/" -SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" - -LICENSE="GPL-3" -SLOT="2" -KEYWORDS="amd64 x86" - -IUSE="examples cpu_flags_x86_sse2 +tbb" - -RDEPEND="dev-lang/perl" -DEPEND="${RDEPEND} - app-arch/unzip - tbb? ( dev-cpp/tbb )" - -S="${WORKDIR}/${PN}2-${PV}" - -DOCS=( AUTHORS NEWS TUTORIAL ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -pkg_pretend() { - if ! use cpu_flags_x86_sse2 ; then - eerror "This package requires a CPU supporting the SSE2 instruction set." - die "SSE2 support missing" - fi -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CXX="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS} -msse2" \ - WITH_TBB="$(usex tbb 1 0)" -} - -src_install() { - dobin ${PN}2 ${PN}2-* - - exeinto /usr/libexec/${PN}2 - doexe scripts/* - - newman MANUAL ${PN}2.1 - einstalldocs - - if use examples; then - insinto /usr/share/${PN}2 - doins -r example - fi -} diff --git a/sci-biology/cufflinks/Manifest b/sci-biology/cufflinks/Manifest index 26e76f6dde26..57016b548680 100644 --- a/sci-biology/cufflinks/Manifest +++ b/sci-biology/cufflinks/Manifest @@ -1,7 +1,9 @@ AUX cufflinks-2.2.1-boost-1.65-tr1-removal.patch 344 BLAKE2B af0287f43bfd37da352fc330e3f6e06d4c6946851c6d8760302078157c8073591ccf7b508e2debf35747837216cc15e952fd7128bca500547cc180061dc2f780 SHA512 774558e93cf57ca9e9361df2271119474c8726573ff4467af4836db863d87ff0f38fe7048c9287227f18d3541891bb7b433b5fa33567616eeecda2bb5b057e9a AUX cufflinks-2.2.1-flags.patch 1132 BLAKE2B 675fb86a95425ed0def259b6f316e443eddb0c80a3a4f78e724f85ca3b14e58c29bb59bbc80a61ee7dcfaeb404383ffe0e58669dedc95224913c8d43939fd799 SHA512 58ea036d55d0b4835a56ea66afc2359bdb3e022f1fda3cab8402e4a2d7c6eab00fae96c739f89a25ca1e7528dad02f20c5c944a198c1eeca245e8995fbaa8f12 +AUX cufflinks-2.2.1-format-security.patch 618 BLAKE2B 1a316055af35849333c8ccbd46079a4ee1096becde474151932317bb66f81eff27b80d15306d9432f69a42fa9202a7712f9eff9921b915a92f4094ad2eadc79b SHA512 61a8cfe31988b028636f97db06d6855d9fce4ff3548da70d7e791fde85b38c09376be63714b67a0dc3e112f1d543735a51ebc437fc0b32eff98e9bf13138ff3c AUX cufflinks-2.2.1-gcc6.patch 344 BLAKE2B 7534c9060e93f074718726e2cbf7df259ba298b447915a4162916977340d33e35a4fddbf3e1b662334b56d42ffb8e0a096c337b465b5952abe27d1248fd6d0f2 SHA512 1e8fc2e717c464e39aecf2c434857e962a809fd2a9f84bfca2b7230d5150d464262b579f1a8c13970767e929562d04994d60002834c98c204e089d2d2a8381c0 +AUX cufflinks-2.2.1-gcc7.patch 4133 BLAKE2B ac2fbf2ebadfe0e90d7163dbd839b2173a3a3a9925b25e2eba8775793545ed8e17e8075c9e562300fa0fae6fd7c35893c8bc892c3e79bd6645b2e3cf51acbdbf SHA512 cbcc2be9e1266e24801dc91ed776aa314761ac682274c103c4f4ad9c37f8ad02b63233f2a16608dd620ca67e89a21028142bdc059cbe5fd2fffdbdb3e38f0af8 AUX cufflinks-2.2.1-samtools-legacy.patch 1105 BLAKE2B ceeb2236456f30598e0d98ce1eaa4fae908286704fb6912a19ccc008b3d41476b853cacc3fc545450dde7d883593a545110a440c044118875041f56077c963b3 SHA512 80c6eaadcfe6919d61b63efc83d3d618e939c3a1cd5e4977f936c41656a96c7c2dd71a1309d6b0422b1bf248a366643a62f011b30b37b4001efae5da04acaadf DIST cufflinks-2.2.1.tar.gz 766280 BLAKE2B 200ca88d15cdfca550a12a39cf69d4c41850532c76840d2a86a21654b317e28c7f35d36ba26105490e75d55c5527dd64da1ef3c14f2d467a60379c234a8e9e60 SHA512 4da7f3a6090ea8cf469a85208c91073abdcd8b0e71c51b0f7052ce8001c368055b9d9cb7726d463196f5b3ab0b4a49bf5241d321ac3fe061225ecc47b4ca209b -EBUILD cufflinks-2.2.1-r2.ebuild 1187 BLAKE2B 6d688f33f3404055c9b0a52a442a1a9f5c0d25a77a55fbdcfad4b521a98c0be66eaa238f341745ec14a9207753547e2c1b24dfaf46e45a46aa6c6b94927cec55 SHA512 8894ed39cc003b86660453968ad4ba7013153e16ec22f7818dce541bcdfd241693139ad45996b8b42edce5412de1413f4ad0966bf5b04c5e9a39476458d14a82 +EBUILD cufflinks-2.2.1-r2.ebuild 1260 BLAKE2B d6a462ebb0ab2851622b70796b6fc436784273004623792c40d95ebcaf0bd6116efe9fc4bfc25ea6fdc8fa1a4bd961564bf32c79e96ab055309df52109c0ca7e SHA512 e18f4e22800d944f71bb498fd6d6de827ef1d6dc3a37b4aabfa9d8c253ee4663cdd3ed6758845f755e3061765cdf9dac1d1f52f5d42da5ccd80449f6f667b9b9 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild index 89f8484fad6a..745baffad99d 100644 --- a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild +++ b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild @@ -31,6 +31,8 @@ PATCHES=( "${FILESDIR}"/${P}-flags.patch "${FILESDIR}"/${P}-gcc6.patch "${FILESDIR}"/${P}-boost-1.65-tr1-removal.patch + "${FILESDIR}"/${P}-gcc7.patch + "${FILESDIR}"/${P}-format-security.patch ) src_prepare() { diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch new file mode 100644 index 000000000000..fa13f78d8b52 --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch @@ -0,0 +1,16 @@ +Author: Andreas Tille <tille@debian.org> +Date: Wed, 22 May 2013 13:27:40 +0200 +Description: When building with --format-security (Debhelper 9 hardening) + this patch is needed to build successfully + +--- a/src/locfit/makecmd.c ++++ b/src/locfit/makecmd.c +@@ -200,7 +200,7 @@ char *cmdline; + /* vs is used to store the command line string. */ + sprintf(vn,"=clstr%d",clcount); + vs = createvar(vn,STSYSTEM,1+strlen(cmdline),VCHAR); +- sprintf((char *)vdptr(vs),cmdline); ++ sprintf((char *)vdptr(vs),"%s",cmdline); + + /* va is used to store pointers to the command line fields. */ + sprintf(vn,"=cline%d",clcount); diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch new file mode 100644 index 000000000000..48fe6e10ac96 --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch @@ -0,0 +1,121 @@ +Author: Alex Mestiashvili <mailatgoogl@gmail.com> +Origin: https://lists.debian.org/debian-med/2017/09/msg00021.html +Bug-Debian: https://bugs.debian.org/871234 +Description: Fix gcc-7 build issue, thanks to Jeff Epler <jepler@unpythonic.net> +--- a/src/GHash.hh ++++ b/src/GHash.hh +@@ -88,7 +88,7 @@ + //nextkey is SET to the corresponding key + GHashEntry* NextEntry() { //returns a pointer to a GHashEntry + register int pos=fCurrentEntry; +- while (pos<fCapacity && hash[pos].hash<0) pos++; ++ while (pos<fCapacity && (hash[pos].hash)<0) pos++; + if (pos==fCapacity) { + fCurrentEntry=fCapacity; + return NULL; +@@ -186,7 +186,7 @@ + x=HASH2(h,n); + GASSERT(1<=x && x<n); + while(k[p].hash!=-1) p=(p+x)%n; +- GASSERT(k[p].hash<0); ++ GASSERT((k[p].hash)<0); + k[p]=hash[i]; + } + } +@@ -225,7 +225,7 @@ + GTRACE(("GHash::insert: key=\"%s\"\n",ky)); + //GMessage("GHash::insert: key=\"%s\"\n",ky); + GASSERT(0<=i && i<fCapacity); +- GASSERT(hash[i].hash<0); ++ GASSERT((hash[i].hash)<0); + hash[i].hash=h; + hash[i].mark=mrk; + hash[i].key=Gstrdup(ky); +@@ -266,7 +266,7 @@ + GTRACE(("GHash::insert: key=\"%s\"\n",ky)); + //GMessage("GHash::insert: key=\"%s\"\n",ky); + GASSERT(0<=i && i<fCapacity); +- GASSERT(hash[i].hash<0); ++ GASSERT((hash[i].hash)<0); + hash[i].hash=h; + hash[i].mark=mrk; + hash[i].key=(char *)ky; +@@ -310,7 +310,7 @@ + if(i==-1) i=p; + GTRACE(("GHash::replace: %08x: inserting: \"%s\"\n",this,ky)); + GASSERT(0<=i && i<fCapacity); +- GASSERT(hash[i].hash<0); ++ GASSERT((hash[i].hash)<0); + hash[i].hash=h; + hash[i].mark=mrk; + hash[i].key=Gstrdup(ky); +@@ -412,7 +412,7 @@ + + template <class OBJ> char* GHash<OBJ>::NextKey() { + register int pos=fCurrentEntry; +- while (pos<fCapacity && hash[pos].hash<0) pos++; ++ while (pos<fCapacity && (hash[pos].hash)<0) pos++; + if (pos==fCapacity) { + fCurrentEntry=fCapacity; + return NULL; +@@ -425,7 +425,7 @@ + + template <class OBJ> OBJ* GHash<OBJ>::NextData() { + register int pos=fCurrentEntry; +- while (pos<fCapacity && hash[pos].hash<0) pos++; ++ while (pos<fCapacity && (hash[pos].hash)<0) pos++; + if (pos==fCapacity) { + fCurrentEntry=fCapacity; + return NULL; +@@ -439,7 +439,7 @@ + + template <class OBJ> OBJ* GHash<OBJ>::NextData(char* &nextkey) { + register int pos=fCurrentEntry; +- while (pos<fCapacity && hash[pos].hash<0) pos++; ++ while (pos<fCapacity && (hash[pos].hash)<0) pos++; + if (pos==fCapacity) { + fCurrentEntry=fCapacity; + nextkey=NULL; +@@ -457,16 +457,16 @@ + // Get first non-empty entry + template <class OBJ> int GHash<OBJ>::First() const { + register int pos=0; +- while(pos<fCapacity){ if(0<=hash[pos].hash) break; pos++; } +- GASSERT(fCapacity<=pos || 0<=hash[pos].hash); ++ while(pos<fCapacity){ if(0<=(hash[pos].hash)) break; pos++; } ++ GASSERT(fCapacity<=pos || 0<=(hash[pos].hash)); + return pos; + } + + // Get last non-empty entry + template <class OBJ> int GHash<OBJ>::Last() const { + register int pos=fCapacity-1; +- while(0<=pos){ if(0<=hash[pos].hash) break; pos--; } +- GASSERT(pos<0 || 0<=hash[pos].hash); ++ while(0<=pos){ if(0<=(hash[pos].hash)) break; pos--; } ++ GASSERT(pos<0 || 0<=(hash[pos].hash)); + return pos; + } + +@@ -474,8 +474,8 @@ + // Find next valid entry + template <class OBJ> int GHash<OBJ>::Next(int pos) const { + GASSERT(0<=pos && pos<fCapacity); +- while(++pos <= fCapacity-1){ if(0<=hash[pos].hash) break; } +- GASSERT(fCapacity<=pos || 0<=hash[pos].hash); ++ while(++pos <= fCapacity-1){ if(0<=(hash[pos].hash)) break; } ++ GASSERT(fCapacity<=pos || 0<=(hash[pos].hash)); + return pos; + } + +@@ -483,8 +483,8 @@ + // Find previous valid entry + template <class OBJ> int GHash<OBJ>::Prev(int pos) const { + GASSERT(0<=pos && pos<fCapacity); +- while(--pos >= 0){ if(0<=hash[pos].hash) break; } +- GASSERT(pos<0 || 0<=hash[pos].hash); ++ while(--pos >= 0){ if(0<=(hash[pos].hash)) break; } ++ GASSERT(pos<0 || 0<=(hash[pos].hash)); + return pos; + } + diff --git a/sci-biology/dialign-tx/Manifest b/sci-biology/dialign-tx/Manifest index f6accfd6b989..443791cbbb26 100644 --- a/sci-biology/dialign-tx/Manifest +++ b/sci-biology/dialign-tx/Manifest @@ -1,5 +1,7 @@ -AUX dialign-tx-1.0.2-implicits.patch 776 BLAKE2B e91b85b42d9e61d4895ff34f2a6d7e869cc32edc6a8e6aee0378a3083cd1d3d4e148f6b223d60a3456a5db0b07859cd63c8d624060b365d5b13a6d75fd98983d SHA512 632da19c24834f011778e1be23a8b19f64da4e52386c99838393f678e927174bd8d3d9d175716e2651fcb884673123136166c401d3e687b882e5eaf69d597a1b +AUX dialign-tx-1.0.2-fix-build-system.patch 588 BLAKE2B 3d9757b2b66497a47bfc3412a1e014f85e0dd12c2247103c813f3406ae0b34e8ba8a68cf31481f9f184095c07e63840fa2643c04a34a3e3f2605b90b2e8bba50 SHA512 30a474f59fb18dcef572299aa6bb6a22d9d6188193a3341bd04c32d6c388358e890ea17bcb8fd31fe80cee58330be6cb004b5936bf98d204e6f5a1e40627bf4f +AUX dialign-tx-1.0.2-gnu89-inline.patch 493 BLAKE2B d37822818faabfa55cfd0a32cf0c0f22548ff29eb7c55712b1ef8e4fe4652531cfe821236e206a7bdaec74c4cac22e5d519be41f282b717d2119d7a79e478e44 SHA512 ad63585d93a10b44b1ca810b4a1bbbd991cc5fb1e762b941931d28f50dcc6a2bb6fdedea7c5faedcf4b2452dc8b99374423752694c5aa0a481ce5e97d8f5d3dd +AUX dialign-tx-1.0.2-implicits.patch 780 BLAKE2B b6eb50c7eaecf6439a1d27a0173661efef100a10976abf521fe50a4687d7e89e0cb094693118a84e68daae3918708ee3323073299d3d28786031a1f41c39af75 SHA512 783afc4527e0a77f0aac66bd8aa00ce3e5ddd81dd652c7459e551c609755eb3b0bd5b02566d8d1636b8840ed8567bb5652866c41ecf038ac9fe5682e1edf3e64 AUX dialign-tx-1.0.2-modernize.patch 6149 BLAKE2B f6f3044b38d4652c2bc3aa63714beb42220ac00d0ecfe68b692b7af0f6dc1d29a8d053962d324e33bf32df2b92bd0fad40b5ec352ae837f6eaba1920f73d8d90 SHA512 cf1c1200500eb3e5f159468fe52536e8ffff60de21e09bb81e585270224ac4ce93d59fe80bd5a8212a4154ad90b23ec415be11b42792440c7fd53f75762d047a DIST DIALIGN-TX_1.0.2.tar.gz 1765296 BLAKE2B 3cce811a58fcf210f42c4a783e8ebb56c66436912ff04bce270058193f0d7b21114d75e2d67829c7abfbb35814e5a16f7f952611729ab211d066403a411db94a SHA512 ff43f1f2900bdd12b7a8ba382a4d6ad68e6c2e6d7ceb1a65f0e571bb891cc2dc2661fb6ce698aaabf0e20c14565b5927ae0076a7170c8611679f936851a00c43 -EBUILD dialign-tx-1.0.2-r1.ebuild 998 BLAKE2B 3f5bb90b5fb4729c351f7aea6475b849353e33dd6428b437e16b9dc1d884201d9a528c1ae551675f7a3acb48f0983a204bdac5cb1e892cdcf10a65b19d186ada SHA512 7baa791bc863006cf66828bf3a08ec87afe03f72ba181280f5e26cf826a939bcc854bb94b40551f11a818006dae3a229db15f61b09f11438dece536e150b0ad0 +EBUILD dialign-tx-1.0.2-r2.ebuild 950 BLAKE2B 127ba32952e662b90c43dd901f4fe8aa1f6bb99d57adfc39b3bc65dfc9b52ece3809386b3fa2bf4ee649c83b5cc93306930b995ced48f586edbbb85c551a55d2 SHA512 813f6a5337e0c390ef57eedbbb80b9553f0f9bc81fbdbed58d4572e7a3d8d830b15ed54aa9033fadfa49157fcee94ec43396b9cd1c03d9889079fb2d4267cf15 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild b/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild index 2f63ea80bb45..123977916f06 100644 --- a/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild +++ b/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=6 -inherit eutils multilib toolchain-funcs +inherit toolchain-funcs -MY_P=DIALIGN-TX_${PV} +MY_P=${PN^^}_${PV} DESCRIPTION="Greedy and progressive approaches for segment-based multiple sequence alignment" HOMEPAGE="http://dialign-tx.gobics.de/" @@ -13,32 +13,33 @@ SRC_URI="http://dialign-tx.gobics.de/${MY_P}.tar.gz" LICENSE="LGPL-2.1" SLOT="0" -KEYWORDS="amd64 x86" -IUSE="" +KEYWORDS="~amd64 ~x86" S=${WORKDIR}/${MY_P} - -src_prepare() { - sed -e "s/\$(CC) -o/\$(CC) \$(LDFLAGS) -o/" \ - -i source/Makefile || die #336533 - epatch "${FILESDIR}"/${P}-implicits.patch \ - "${FILESDIR}"/${P}-modernize.patch +PATCHES=( + "${FILESDIR}"/${P}-fix-build-system.patch + "${FILESDIR}"/${P}-implicits.patch + "${FILESDIR}"/${P}-modernize.patch + "${FILESDIR}"/${P}-gnu89-inline.patch +) + +src_configure() { + tc-export CC } src_compile() { emake -C source clean - emake -C source CC="$(tc-getCC)" \ - CPPFLAGS="" + emake -C source } src_install() { - dobin "${S}"/source/dialign-tx + dobin source/dialign-tx insinto /usr/$(get_libdir)/${PN}/conf - doins "${S}"/conf/* + doins -r conf/. } pkg_postinst() { einfo "The configuration directory is" - einfo "${ROOT}usr/$(get_libdir)/${PN}/conf" + einfo "${EROOT%/}/usr/$(get_libdir)/${PN}/conf" einfo "You will need to pass this to ${PN} on every run." } diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fix-build-system.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fix-build-system.patch new file mode 100644 index 000000000000..cbfd458043c5 --- /dev/null +++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fix-build-system.patch @@ -0,0 +1,24 @@ +--- a/source/Makefile ++++ b/source/Makefile +@@ -1,4 +1,3 @@ +-CC=gcc
+ # debug
+ #CPPFLAGS=-g -O0 -Q -v -da
+ #CPPFLAGS=-g -O0 -fstack-check -Q -v -da
+@@ -8,7 +7,6 @@ + # THIS IS FOR THE OPTIMIZED ONE
+ #CPPFLAGS=-g
+ #CPPFLAGS=-O3 -march=i686 -funroll-loops
+-CPPFLAGS=-O3 -funroll-loops -march=i686 -mfpmath=sse -msse -mmmx
+ #CPPFLAGS=-march=athlon-mp -g -O0 -Wall -D_USE_XOPEN -D__unix__
+
+ OBJ_DIR=.
+@@ -33,7 +31,7 @@ +
+ museq: $(OBJ)
+ rm -f $(TARGET)/$@
+- $(CC) -o $(TARGET)/$@ \
++ $(CC) $(LDFLAGS) -o $(TARGET)/$@ \
+ $(OBJ) \
+ -pipe -Wall -lm
+ mv museq dialign-tx
diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch new file mode 100644 index 000000000000..21f576f07052 --- /dev/null +++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch @@ -0,0 +1,11 @@ +--- a/source/diag.c ++++ b/source/diag.c +@@ -958,7 +958,7 @@ + * The pointer returned (and the ones included in the struct) + * has to be deallocted explicitely from memory. + */ +-inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix, ++static inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix, + struct prob_dist *pdist, struct seq* seq1, + struct seq* seq2, struct alignment *algn, + long double **tmp_dist, int round) { diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch index a8388d03232f..d82a5bf4be33 100644 --- a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch +++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch @@ -1,5 +1,5 @@ ---- source/museq.c -+++ source/museq.c +--- a/source/museq.c ++++ b/source/museq.c @@ -38,6 +38,7 @@ //extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, // struct prob_dist *pdist); diff --git a/sci-biology/dialign2/Manifest b/sci-biology/dialign2/Manifest index ae948999dfa1..4b256f8e8838 100644 --- a/sci-biology/dialign2/Manifest +++ b/sci-biology/dialign2/Manifest @@ -1,3 +1,4 @@ +AUX dialign2-2.2.1-fix-build-system.patch 819 BLAKE2B c639532a8bc95744c91f07f0e672255110b31e2964bb8bfbacaa6b401dcee6a10e29199d9a19614f690a610109c2a5f0ab785b66c144373ceb4724112182cab2 SHA512 8a85911d1743c186f3dea402333e502cfd4f7807065277a2657d790ab9cf1c8d535fbb25abf994f83cdab9849d4ec203d8db8198cf10fa91996d61b63d98f807 DIST dialign-2.2.1-src.tar.gz 209015 BLAKE2B daf903b735e164879a8ceb998ca5ea0c5243927d9b88b4041633af06da7d1f608d58933ee098393e99093b7d11587a59277d9d0927214df0341a8a623b0d5608 SHA512 eb51fbc8d81e384ac19e9cc957be233287a1d81a7f020d77ab16ee6943382bd4e81099c0c9028fcff130def62cdf19de59e9a9c08ea4cb67b9d8f1939eb3bc45 -EBUILD dialign2-2.2.1.ebuild 756 BLAKE2B 32e2636c7df60a877c1c1f84f9ec83d41f8a15d293b5a91808790b613ae5b0be4b09c562b4ed4be47cc5839a79259b05af66abc3056fc519d597b29e0e56db95 SHA512 ead9440fc5b4bbbed8ca6b6dd39ac57dfe8da4d2556c864ecddaf2b2f94589c95fd5fe82fc6ce45cab11eb8a197324b5cc89d38b0ca2c4f10741c3639799bbc3 +EBUILD dialign2-2.2.1.ebuild 836 BLAKE2B abb98cbbfcfe09ead711558bb07b41dcd79aa706793d1aadff9eb258daac8bd42ccbef2fbb74602b0e71bc99aa863a749b0239d63c23edc78982116e4febcf0e SHA512 6714a835544683e1b135ee65aa0728e1f2943349358b4d1505c583f1beba3b4210f3fdec01625ef8bf7a92605274f47233e7ce630cd9a2996e77a098d1990e51 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/dialign2/dialign2-2.2.1.ebuild b/sci-biology/dialign2/dialign2-2.2.1.ebuild index 13ce733d8a79..db310e3fe8d3 100644 --- a/sci-biology/dialign2/dialign2-2.2.1.ebuild +++ b/sci-biology/dialign2/dialign2-2.2.1.ebuild @@ -1,34 +1,37 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=6 -inherit toolchain-funcs +inherit flag-o-matic toolchain-funcs DESCRIPTION="Multiple sequence alignment" HOMEPAGE="http://bibiserv.techfak.uni-bielefeld.de/dialign" -SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/dialign/resources/downloads/dialign-2.2.1-src.tar.gz" +SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/dialign/resources/downloads/dialign-${PV}-src.tar.gz" -SLOT="0" LICENSE="LGPL-2.1" +SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" -S="${WORKDIR}"/dialign_package +S=${WORKDIR}/dialign_package +PATCHES=( "${FILESDIR}"/${PN}-2.2.1-fix-build-system.patch ) + +src_configure() { + tc-export CC + append-cppflags -I. -DCONS +} src_compile() { - emake -C src \ - CC="$(tc-getCC)" \ - CFLAGS="${CFLAGS} -I. -DCONS -c" + emake -C src } src_install() { dobin src/${PN}-2 insinto /usr/share/${PN} - doins dialign2_dir/* + doins -r dialign2_dir/. - cat >> "${T}"/80${PN} <<- EOF - DIALIGN2_DIR="${EPREFIX}/usr/share/${PN}" + cat >> "${T}"/80${PN} <<- EOF || die + DIALIGN2_DIR="${EPREFIX}/usr/share/${PN}" EOF doenvd "${T}"/80${PN} } diff --git a/sci-biology/dialign2/files/dialign2-2.2.1-fix-build-system.patch b/sci-biology/dialign2/files/dialign2-2.2.1-fix-build-system.patch new file mode 100644 index 000000000000..45365c56e3a4 --- /dev/null +++ b/sci-biology/dialign2/files/dialign2-2.2.1-fix-build-system.patch @@ -0,0 +1,46 @@ +--- a/src/makefile ++++ b/src/makefile +@@ -10,8 +10,6 @@ + ############################### + + +-CC = gcc +-CFLAGS = -c -O -I$ -DCONS + #CFLAGS = -g -c -I$ -DCONS + LIBS = -lm + # +@@ -23,33 +21,4 @@ + + # + dialign2-2: $(OBJS) +- $(CC) $(OBJS) $(LIBS) -o dialign2-2 +-# $(CC) -g $(OBJS) $(LIBS) -o dialign2-2_db +-# +-# +-# Subroutines +-# +- +-dialign.o: dialign.c +- $(CC) $(CFLAGS) dialign.c +-functions.o: functions.c +- $(CC) $(CFLAGS) functions.c +-input.o: input.c +- $(CC) $(CFLAGS) input.c +-frag_chain.o: frag_chain.c +- $(CC) $(CFLAGS) frag_chain.c +-para.o: para.c +- $(CC) $(CFLAGS) para.c +-output.o: output.c +- $(CC) $(CFLAGS) output.c +-wgt.o: wgt.c +- $(CC) $(CFLAGS) wgt.c +-regex.o: regex.c +- $(CC) $(CFLAGS) regex.c +-anchor.o: anchor.c +- $(CC) $(CFLAGS) anchor.c +- +-# +- +- +- ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS) diff --git a/sci-biology/mosaik/Manifest b/sci-biology/mosaik/Manifest index 0a6c6c678ede..e70550f4ed6a 100644 --- a/sci-biology/mosaik/Manifest +++ b/sci-biology/mosaik/Manifest @@ -1,6 +1,7 @@ AUX mosaik-2.2.30-Wformat-security.patch 3296 BLAKE2B f75a4dde6fb88e0175989ff9ddfd6dfd2450eb0df24e4e5f60943fbd9fcc40b798d7d7bca2d57e25c4201f6a7cbf8eb66b2f3573f54fc05b5b3a46e3e01a1ddb SHA512 e72fa7cac8798425ac1dd4d3358bfdff640cc831a01531749ee2fad99f8b53bd64e8c7fcdddce205e9f6dd312cc74376afcba395ab8d508d92416190b7eed1df AUX mosaik-2.2.30-fix-build-system.patch 8056 BLAKE2B 4c795e790718dca2a46e25fd67499612ad1226c6e6ad73d7543cd1c1aa1dacabc0ed77ade798b2602d8f661eeb9cd7b033bd8945d4384d01e2d279762f40fa14 SHA512 ed4a6efd9fb2fabd6c24adaa5894fde80024d8ee930450711c07388b62969a41e801f052ee88d7890355f1ddfc5ef9fbb40bfdabfbfae364c64c673ce08958c6 +AUX mosaik-2.2.30-gcc7.patch 1252 BLAKE2B 896d662807c223cc69eacfa2e1fcb457c696e0d198dfa718f0f7eb9060d9c0491a18017901385227c2c0906e02c61a8fb9a9deb71f228d4c6195cdf0b5696515 SHA512 fc7dd31d2fcce7a4e624e759ee08b8997757bf4ce3ae3f98080e6e6252dfc647de4848f6a736b35090e8c8da37618baaf08e19be9ddfc408bbc5f7200f44cbba AUX mosaik-2.2.30-remove-platform-code.patch 399 BLAKE2B ec711a9b112efa87b2811e4545bfc58716393576915f71167ff700ccd809be4fad5e07bac7a5cb7df911615f4c996284cd711c1d1cb62c5a18695e719e6574c6 SHA512 4aec709660b41fb61bb9219a587255a5f416992a4478c2a7eb67374d1425f0a4e0b4d356827a9214e2f2718b635169c95d3288bf10388a74e50d498c39c2f259 DIST mosaik-2.2.30.tar.gz 4387062 BLAKE2B 6f373aeae4f68be2455556e7f79a5850e25d804bd482d85a846b44f8adaabb2513ffc7ced774f5ead6dbc8fc9dca9d64f76f83bc5b55b1be4073a8cf309e121b SHA512 1acf534e6defc927fc22937a7bae6786e85ab7aa234b4209169f1267f1a9bd68415b441c6aed2e7cd667f694a562017ebc9457251958f77386259ffce9812b10 -EBUILD mosaik-2.2.30.ebuild 1104 BLAKE2B a567a6ce6f232eff13980b0d1d9ad54f4ff486539c8bbb594412c4dd8798e59ca23df40af0acd93d17f552683b39adc6e0212e8c09ab308d186206c6dfa225f3 SHA512 34863af564b085b85d1670b9c20fdc8ca8c5367e210a041c81d2cb67e5380e91636620214ebe06c347cb0ac556581d304374e527738c36b01029cf38a4846a4b +EBUILD mosaik-2.2.30.ebuild 1105 BLAKE2B 842b161c8fc0cda9cab8101ca6ae0879cedb191983a61a25d21afe0ef5edb4a87e7e62edad27f2642444c2dc58387328c275f7830abd7917146d6febee812ba5 SHA512 55377965262d7942229a269bc1c0c56ff930d544b422305994f0995ca68d06ea3a1745fb759dc70225ff6b76d338b8761236079eb7107edb6225ae7c6d2f372e MISC metadata.xml 414 BLAKE2B 3c19ab9f4c6a0f4e73d67fe4f280fd252d68120a28e045a39c3ad78a4741921b2141c4433c6babcdc33b16083d4949fc28448f57fcb6c65be8719dd1d0bff8f3 SHA512 2e6887226a0ac7457d1bbce1d76ac0953f0c1d5ff1d4261b7e11e4fa38803f01f8a67a285c2071671d58fcb8912ca8bb66bdfca93e2481be043ec5f2f2353c5b diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-gcc7.patch b/sci-biology/mosaik/files/mosaik-2.2.30-gcc7.patch new file mode 100644 index 000000000000..ebf925a0cbb7 --- /dev/null +++ b/sci-biology/mosaik/files/mosaik-2.2.30-gcc7.patch @@ -0,0 +1,40 @@ +--- a/CommonSource/ExternalReadFormats/BamWriter.cpp ++++ b/CommonSource/ExternalReadFormats/BamWriter.cpp +@@ -496,7 +496,7 @@ + buffer[6] = 0xffffffff; // mate_pos + buffer[7] = 0; // ins_size + +- const char* startChar = '\0'; ++ const char* startChar = NULL; + + // write the block size + const unsigned int dataBlockSize = nameLen + packedCigarLen + encodedQueryLen + queryLen; +@@ -652,7 +652,7 @@ + unsigned int zaTagLen = 0; + string zaTag; + char* pZaTag; +- if ((zaString != 0) && (zaString != (char)0)) { ++ if ((zaString != 0) && (zaString[0] != '\0')) { + zaTagLen = 3 + strlen( zaString ) + 1; + zaTag.resize( zaTagLen ); + pZaTag = (char*)zaTag.data(); +@@ -776,7 +776,7 @@ + BgzfWrite(mdTag.data(), mdTagLen); + + // write the ZA tag +- if ( zaString != 0 && (zaString != (char)0)) ++ if ( zaString != 0 && (zaString[0] != '\0')) + BgzfWrite(zaTag.data(), zaTagLen); + + // write the ZN tag +--- a/MosaikAligner/AlignmentThread.cpp ++++ b/MosaikAligner/AlignmentThread.cpp +@@ -591,7 +591,7 @@ + buffer.al = al; + buffer.noCigarMdNm = noCigarMdNm; + buffer.notShowRnamePos = notShowRnamePos; +- if ( zaString == (char)0 ) ++ if ( zaString == NULL ) + buffer.zaString.clear(); + else + buffer.zaString = zaString; diff --git a/sci-biology/mosaik/mosaik-2.2.30.ebuild b/sci-biology/mosaik/mosaik-2.2.30.ebuild index 45633c47dab5..874edba4504d 100644 --- a/sci-biology/mosaik/mosaik-2.2.30.ebuild +++ b/sci-biology/mosaik/mosaik-2.2.30.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -11,18 +11,15 @@ SRC_URI="https://github.com/wanpinglee/MOSAIK/archive/5c25216d3522d6a33e53875cd7 LICENSE="GPL-2" SLOT="0" -IUSE="" KEYWORDS="~amd64 ~x86" -DEPEND="" -RDEPEND="" - S="${WORKDIR}/${P}/src" PATCHES=( - "${FILESDIR}/${P}-remove-platform-code.patch" - "${FILESDIR}/${P}-fix-build-system.patch" - "${FILESDIR}/${P}-Wformat-security.patch" + "${FILESDIR}"/${P}-remove-platform-code.patch + "${FILESDIR}"/${P}-fix-build-system.patch + "${FILESDIR}"/${P}-Wformat-security.patch + "${FILESDIR}"/${P}-gcc7.patch ) src_configure() { diff --git a/sci-biology/primer3/Manifest b/sci-biology/primer3/Manifest index 98e896ecef04..75cde6014283 100644 --- a/sci-biology/primer3/Manifest +++ b/sci-biology/primer3/Manifest @@ -1,8 +1,5 @@ AUX primer3-2.3.4-buildsystem.patch 5460 BLAKE2B 1e7680501e9c4a74c599f52caa787751f74f6a4fd028d8273d00364c7d2e59c0a641d343386e6ff7598d7d0bbfa66ce80412d300646cd54d0112ce118ff8422d SHA512 52f539f52c92e5e21c3166da62813c6fa9f90fd9e0ca87d9ab67658496e13f4b5ce5c53770802cb1cdd21044244e21f09b0de2ce3c6d3db0182b3d9cbf64a037 -DIST primer3-2.3.5.tar.gz 1655871 BLAKE2B 6311a15334adc4121a62a4ff0f42f32f81e147b43742a59d6708c2e64a714c59b019433fcedebf5e88cefd2e46f4879d1f950acc0346f2da73d2567e621056f2 SHA512 e64c27eea0258af913304963254494d6c874e7776b09a14ee9a273f1a3cdfa908acf92b78affc0102f06df17effbf011181c60d97ebd0a645044df7a28b41fec +AUX primer3-2.3.7-gcc7.patch 421 BLAKE2B 3f861ecb493ce9673cdebac9ea224a0588bd3b758d72a7ef4e41d4efb929db444a8c2808a55ead42dcb174265a926c021a89dd83dc8a1e5ba4eb5ed26280be43 SHA512 c818cd80e4762ef46e4e52acd27f4eb966d676995154b3503c98d8defb545c3dd7ea307c8946b5b5c462dd7f5dee6abc254cea59e21e2229cb779a7178dec04d DIST primer3-2.3.7.tar.gz 1658090 BLAKE2B 0bc9a0faa19c4ac3b48680d65b0d91a13d8bdd651ad3a0d344b4f50ce8dc510fe7a22665192751fb2c8ff6282b560daf4540a02cc70482dba0fcc344f7727e37 SHA512 f227f80d395cb682a9d65e0ac3afdcacb8385d66e721b9163fda939a9c788a7c6907273f6223782702b48d7df66ea2331114f6303fcd29e3b3c50a2717da2fa7 -DIST primer3-src-2.3.6.tar.gz 1667573 BLAKE2B 02344f1f13a639654ec040c893691c132193f81d2c64588a6ac1556f268d6768307bf12f77580aa8096f35f95401caebecfa080135bbb75bff4fac30120cc4a9 SHA512 671b420f3bc9b6b9972e19a757925ada170e5f8c0e3e8a90630a48e6cde44abc0e1e09b9ea90129f94b58f835e30440f3d91c14fb4b796fd94eb478b2ca28ead -EBUILD primer3-2.3.5.ebuild 1029 BLAKE2B 5a0c27b029fffdfed3851928c65c6936c981eaf6b5b70322120427165eeb58078b13957b4288b4642b952854d3e8119d80914e1d36fa427bfb2a0b5a2d18f152 SHA512 a52d99dde78f30879e6d109d36d5d2d258494d5dda1548b78044731decd772ccf78c0203dc1844a4c08b96f26ac52671da4b11efdbb732a578c45cf31b68119a -EBUILD primer3-2.3.6.ebuild 1040 BLAKE2B 93acf2275975e9af3e27f328624ea3e5931da124fc009f95f604217de212cab23b96afa5191daf2d7a47eb329dcedb0bc5b154edb7a78df617c22d97213a81e7 SHA512 f0471de087faa4e41123c94a1ef6dd32635edd5482d05724e135f8b05bcc073475206256e17f4547bbd269fbcc564f89dc0b4ff8aec33888c9095abcdc7c951d -EBUILD primer3-2.3.7.ebuild 1072 BLAKE2B bc629de01b3d1fe7de243d8c16c6eecd89ba87074058cd0368e43ff4cffcb8b97f5b30e8e5d7386da84b93bd1e56f46f1c338b3d715e138b9d3c9294178e8da3 SHA512 0ba2a4ff56a4ecc8abd17888acd22275f8330418d250503def828f83b047bf84d6a17224e65de75199923b40e95926128a885419b65325a09c061cdeba30f05f +EBUILD primer3-2.3.7.ebuild 1116 BLAKE2B 1aff6985a9ad3ad0ee523f18061c7f31bd26d3cc6c72f440a15c0ae2bc21f84ad360f51b021079efde09ef386f1c92f4dec7d155b970247e9ee87c376e0b36ee SHA512 56b127a7282b1c9dcc514758899d46e23ad79178f402beee270a03959eb01ae28e03720fba1c4dfbfc050e2932a15f5e2254705a048acf8ef8f7db0998327e61 MISC metadata.xml 797 BLAKE2B 169e1065192fa4173181d9ee76a95ee83aefd398627ee65952eb14c3d3db93910c3d2239fe5ca7ce7c68f00e005bd7902a150640b85143f0f9d53fec41392318 SHA512 3d8707f6c780f3bec419c4cdf8564bf3634c4b75e4e7dffebdc29684dfbe89d9404c405e5c7b72e32fc493517e8fa36137c7a6f2b237f788fc6fb46ca43d2f7f diff --git a/sci-biology/primer3/files/primer3-2.3.7-gcc7.patch b/sci-biology/primer3/files/primer3-2.3.7-gcc7.patch new file mode 100644 index 000000000000..a04ee1ac3b12 --- /dev/null +++ b/sci-biology/primer3/files/primer3-2.3.7-gcc7.patch @@ -0,0 +1,17 @@ +--- a/src/thal.c ++++ b/src/thal.c +@@ -426,12 +426,12 @@ + "Illegal type"); + o->align_end_1 = -1; + o->align_end_2 = -1; +- if ('\0' == oligo_f) { ++ if ('\0' == oligo_f[0]) { + strcpy(o->msg, "Empty first sequence"); + o->temp = 0.0; + return; + } +- if ('\0' == oligo_r) { ++ if ('\0' == oligo_r[0]) { + strcpy(o->msg, "Empty second sequence"); + o->temp = 0.0; + return; diff --git a/sci-biology/primer3/primer3-2.3.5.ebuild b/sci-biology/primer3/primer3-2.3.5.ebuild deleted file mode 100644 index 513c7cb5a1a3..000000000000 --- a/sci-biology/primer3/primer3-2.3.5.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils toolchain-funcs - -DESCRIPTION="Primer Design for PCR reactions" -HOMEPAGE="http://primer3.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${PV}/${P}.tar.gz" - -SLOT="0" -LICENSE="GPL-2" -IUSE="" -KEYWORDS="amd64 ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" - -DEPEND="dev-lang/perl" -RDEPEND="" - -src_prepare() { - epatch "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch - - if [[ ${CHOST} == *-darwin* ]]; then - sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die - fi - - tc-export CC CXX AR RANLIB -} - -src_compile() { - emake -C src -} - -src_test () { - emake -C test | tee "${T}"/test.log - grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log" -} - -src_install () { - dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core} - dodoc src/release_notes.txt example - insinto /opt/primer3_config - doins -r src/primer3_config/* primer3*settings.txt - dohtml primer3_manual.htm -} diff --git a/sci-biology/primer3/primer3-2.3.6.ebuild b/sci-biology/primer3/primer3-2.3.6.ebuild deleted file mode 100644 index 21a466681109..000000000000 --- a/sci-biology/primer3/primer3-2.3.6.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils toolchain-funcs - -DESCRIPTION="Primer Design for PCR reactions" -HOMEPAGE="http://primer3.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${PV}/${PN}-src-${PV}.tar.gz" - -SLOT="0" -LICENSE="GPL-2" -IUSE="" -KEYWORDS="amd64 ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" - -DEPEND="dev-lang/perl" -RDEPEND="" - -src_prepare() { - epatch "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch - - if [[ ${CHOST} == *-darwin* ]]; then - sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die - fi - - tc-export CC CXX AR RANLIB -} - -src_compile() { - emake -C src -} - -src_test () { - emake -C test | tee "${T}"/test.log - grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log" -} - -src_install () { - dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core} - dodoc src/release_notes.txt example - insinto /opt/primer3_config - doins -r src/primer3_config/* primer3*settings.txt - dohtml primer3_manual.htm -} diff --git a/sci-biology/primer3/primer3-2.3.7.ebuild b/sci-biology/primer3/primer3-2.3.7.ebuild index d0dbc7363681..4c6c9ce7bf44 100644 --- a/sci-biology/primer3/primer3-2.3.7.ebuild +++ b/sci-biology/primer3/primer3-2.3.7.ebuild @@ -1,30 +1,34 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=6 -inherit eutils toolchain-funcs +inherit toolchain-funcs DESCRIPTION="Primer Design for PCR reactions" HOMEPAGE="http://primer3.sourceforge.net/" SRC_URI="mirror://sourceforge/project/${PN}/${PN}/${PV}/${P}.tar.gz" -SLOT="0" LICENSE="GPL-2" -IUSE="" +SLOT="0" KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" DEPEND="dev-lang/perl" RDEPEND="" -PATCHES=( "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch ) +PATCHES=( + "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch + "${FILESDIR}"/${PN}-2.3.7-gcc7.patch +) src_prepare() { default if [[ ${CHOST} == *-darwin* ]]; then sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die fi +} +src_configure() { tc-export CC CXX AR RANLIB } @@ -32,16 +36,18 @@ src_compile() { emake -C src } -src_test () { +src_test() { emake -C test | tee "${T}"/test.log grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log" } -src_install () { +src_install() { dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core} - dodoc src/release_notes.txt example + insinto /opt/primer3_config - doins -r src/primer3_config/* primer3*settings.txt + doins -r src/primer3_config/. primer3*settings.txt + + dodoc src/release_notes.txt example docinto html dodoc primer3_manual.htm } diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest index 7101d6d36441..a37eb2942b96 100644 --- a/sci-biology/t-coffee/Manifest +++ b/sci-biology/t-coffee/Manifest @@ -1,8 +1,7 @@ +AUX t-coffee-11.00-cxx11.patch 988 BLAKE2B 03caf7bf7a10b22f8dc7e98f672564d4346123f04f8505f4fca040c10cb36031b8891dbe3f661b18f61520ebf48e2c8cc2a53d11b21c44d7d6c06728950e3eba SHA512 d97320c97467b64399ffe5917cbae4e7bac37c57f66eedbaad889f5db60b1da0d57bb4ced716dd97e907f4569789183175e531b10e7577560e18050584dd1598 +AUX t-coffee-11.00-gcc7.patch 864 BLAKE2B a5f18fc86764d69cf584e976e88e4ce08f5299bfa4410ebff5ebf97dd29e8d4995076d921517d05138dbc37525d2e5f370194c0f6962cd4e2ff43bdee7c3f7c1 SHA512 d96c61f5efb1e89750a2fbb2369fdb6d831ad7c093eb2b4237af1ff21528990578399ecc1bb0f1668086084427902922003407eb1bb19f43fa25c0bcc01789a6 AUX t-coffee-11.00-mayhem.patch 1230 BLAKE2B cd54632fb5760f9d76d9e72d69c2d893e0812277c6de7414546a699cf8d98b497273f9ce3f61407181d6c7f0ea0d7720b1de10c02304b92a7d76db3e2732b023 SHA512 b2c232f3e517c9c944c3d13a96b8383f8875e2e968ed16df25e37c6bfeee106cf82f9107187081753fbcaba6e27713fe5f4ca51d2f859ea7e8744f3b2b41f035 AUX t-coffee-11.00-set_proper_dir_permissions.patch 1203 BLAKE2B 220f1932cfab4f3d39cfcf3191754c2a2705c75c9cce8f11d04fb3fe8e3c3e60a10251b01c2109faad2fda4a5ce57ee5e5e598a0ec841c3bb0fa19d0e8e4d636 SHA512 fb19aae00ccc0824bcb757d32ee921159e9ece9c0336b3d663e0140ccfca77bf3fcce0eeb304517e41dc1dd4c9469c345c0c35fe8e7fdf120c6fddba4a4e1524 -AUX t-coffee-9.03.1318-flags.patch 3376 BLAKE2B c578abe18e4ea8b038789c55887c1f1973ff62dc5a9ae28c6b7a959e221d818909bd98b29492b56d64a81c7c408a259b979b4e73f7ef948b605787a61dd2f61e SHA512 db1d4463280a95ce644065c64a653d31d57d144c45afba5ff1dd03911ce3c3c1afb15a29c09b4089558acc364385e3eeddbf9179c662191d730d34e09675243c -DIST T-COFFEE_distribution_Version_11.00.8cbe486.tar.gz 3526354 BLAKE2B fd03894106d09bb95c44fc4f934f99fa6f0b82c56ee9832da2537ebffc12fc9d6e71f1d0371374f397b36852ba85991efb7bdfcc1102737113a35e7943268f68 SHA512 5c486411bae430cfca6f4623f4dff348e2d9ab7c2eb0edef8059c6cb9c01ee48347e06be0c5d19ee1ace4b9f597f19beee8da2d7eecba29c5a78c2aec800be92 -DIST T-COFFEE_distribution_Version_9.03.r1318.tar.gz 3455629 BLAKE2B 2c1c1adb16826b8048f0a92b35d43b0f308aed2e543d2868f9f497c27f19a9d6da5b6bdd72b3b1f7b30783d1efd0e0c7eb51f6cf44f401b4f8149146944fbb5d SHA512 40220c9fca5bee59b66757162ff2279c2ab221cca07532c64ed3606a95a787080cd4d6bf301ca6d20d8ba4f0c2166e5785fc0ad81ed6528eb527f24d59e79cc8 -EBUILD t-coffee-11.00-r1.ebuild 1279 BLAKE2B 884bd4f7397dd7a8f170299d515e137f7773c58046011879b4d98d7da86199a4541c29cbad685221fbf668c02e683461f230922ead73d7beade10dc01a656c42 SHA512 e2e5c6027efc490de8f83bcfdd32fa67ad1b1e40539ccf3e8e2523a7242cdd24621877afaa5f6ed8998e68919faaa439ae8a010638c60c2123b6423cec2a1a3b -EBUILD t-coffee-9.03.1318-r1.ebuild 1335 BLAKE2B 2c4c5aaf24cd09f76643a7d87d942ae2cb699e6f427515454ef2af8e0b6cecc4a1797034b054db4dd2fbf38595274950d02e05d431c75464d4f985e72e229f74 SHA512 92e0607a498f4d84b297d492bf3e12b6565e25ded94e77e6703ea3b5d9745fb1c6cd7d4f8914fd859cf4ccea8c595069669dd47a607901054a344f6c564ab8a2 +DIST T-COFFEE_distribution_Version_11.00.4466924.tar.gz 3502302 BLAKE2B 0d8087eb219ff72e6f478a779ccdb51e7aee861236c522dec5391e854b0b0bf6eab324009686237e6d334d2e13e17700f6692333060a2ed55711380ef2ab2cdb SHA512 c6c1a7b768156f8457dc4c53a77b14ce0b85e591d60762faf6e6f6f3b60dab75e99449d55b42ef3af1c90e244f735e19abb72d0ce871bb9fbfbb8d1641531293 +EBUILD t-coffee-11.00-r2.ebuild 1163 BLAKE2B 7b7dd0de076fa4bb9ac5b59d55df39a118b19f333851beccceeb511f3a780f5bfc2128b29cabd0304320810ea373ed15971eb061604da87d8aeae427876d9167 SHA512 7701957be90259bc4cac73bd3a280d5181432a1d6d30c4223fa4b1c6e497b50ec60b605a5a609068d9139bc3bf3183cf1d1860ece76542952dd3a289996d2b87 MISC metadata.xml 762 BLAKE2B 38e430b2aa0736102b7c8b958c3854723f0d5c88a9301240f9a20d8cdd6f24628ba735aea82d7a379b93d93dc3845e963e9624045933886a2bc09658eaf7827c SHA512 fe31bf756f5e3dbb048e691ecd01ee86000f65ae4f5c19df3c5c3e2deb7fb8ffa83ed39c317188302a8cf2a0d152323a0258497cfb0e3e355dded08b060d0310 diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-cxx11.patch b/sci-biology/t-coffee/files/t-coffee-11.00-cxx11.patch new file mode 100644 index 000000000000..17817d30eca2 --- /dev/null +++ b/sci-biology/t-coffee/files/t-coffee-11.00-cxx11.patch @@ -0,0 +1,21 @@ +--- a/t_coffee_source/programmes_define.h ++++ b/t_coffee_source/programmes_define.h +@@ -390,12 +390,12 @@ + #define XMLSIMPLE_language2 "Perl" + #define XMLSIMPLE_source "empty" + #define XMLSIMPLE_mode "psicoffee,expresso,accurate" +-#define x3dna-ssr_4_TCOFFEE "x3dna" +-#define x3dna-ssr_type "RNA_secondarystructure_predictor" +-#define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" +-#define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" +-#define x3dna-ssr_mode "saracoffee" +-#define x3dna-ssr_update_action "never" ++#define x3dna_ssr_4_TCOFFEE "x3dna" ++#define x3dna_ssr_type "RNA_secondarystructure_predictor" ++#define x3dna_ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ++#define x3dna_ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ++#define x3dna_ssr_mode "saracoffee" ++#define x3dna_ssr_update_action "never" + //TclinkdbEnd + /*New Methods*/ + /********************************************/ diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-gcc7.patch b/sci-biology/t-coffee/files/t-coffee-11.00-gcc7.patch new file mode 100644 index 000000000000..64afc04a4b50 --- /dev/null +++ b/sci-biology/t-coffee/files/t-coffee-11.00-gcc7.patch @@ -0,0 +1,22 @@ +--- a/t_coffee_source/util_lib/aln_convertion_util.c ++++ b/t_coffee_source/util_lib/aln_convertion_util.c +@@ -5592,7 +5592,7 @@ + + list=string2list (H->seq_comment[n]); + if ( list==NULL || atoi(list[0])==1)continue; +- S->seq_comment[a]='\0'; ++ S->seq_comment[a]=NULL; + sprintf (S->name[a], "%s%s%s",H->name[n], list[1], list[2]); + vfree ( S->seq_comment[a]);S->seq_comment[a]=(char*)vcalloc ( strlen (H->seq_comment[n])+1, sizeof (char)); + for (b=3; b< atoi(list[0]); b++)S->seq_comment[a]=strcat (S->seq_comment[a], list[b]); +--- a/t_coffee_source/util_lib/util.c ++++ b/t_coffee_source/util_lib/util.c +@@ -5946,7 +5946,7 @@ + val_array[a]=(char*)vrealloc (val_array[a], strlen (v)+1); + sprintf (val_array[a],"%s",v); + } +- else val_array[a]='\0'; ++ else val_array[a]=NULL; + return v; + } + } diff --git a/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch b/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch deleted file mode 100644 index 5b15108b3bfa..000000000000 --- a/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch +++ /dev/null @@ -1,21 +0,0 @@ - t_coffee_source/makefile | 4 ++-- - 1 file changed, 2 insertions(+), 2 deletions(-) - -diff --git a/t_coffee_source/makefile b/t_coffee_source/makefile -index 9e01ba0..026b714 100644 ---- a/t_coffee_source/makefile -+++ b/t_coffee_source/makefile -@@ -1,6 +1,6 @@ - - t_coffee: util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o -- $(CC) $(CFLAGS) -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o -lm -+ $(CC) $(CFLAGS) $(LDFLAGS) -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o -lm - - all: t_coffee TMalign - -@@ -8,4 +8,4 @@ clean: - rm *.o - - TMalign: -- $(FCC) TMalign.f -o TMalign -+ $(FC) $(FCLAGS) $(LDFLAGS) TMalign.f -o TMalign diff --git a/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild b/sci-biology/t-coffee/t-coffee-11.00-r2.ebuild index 919287c790f8..df1859afb208 100644 --- a/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild +++ b/sci-biology/t-coffee/t-coffee-11.00-r2.ebuild @@ -1,22 +1,21 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=6 -inherit eutils flag-o-matic toolchain-funcs +inherit toolchain-funcs -MY_HASH="8cbe486" +MY_HASH="4466924" MY_PV="${PV}.${MY_HASH}" -MY_P="T-COFFEE_distribution_Version_${MY_PV}" +MY_P="${PN^^}_distribution_Version_${MY_PV}" DESCRIPTION="A multiple sequence alignment package" HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html" -SRC_URI="http://www.tcoffee.org/Packages/Stable/Version_${MY_PV}/${MY_P}.tar.gz" +SRC_URI="http://www.tcoffee.org/Packages/Beta/Latest/${MY_P}.tar.gz" LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" -IUSE="examples" RDEPEND=" sci-biology/clustalw @@ -24,21 +23,22 @@ RDEPEND=" DEPEND="" S="${WORKDIR}/${MY_P}" +PATCHES=( + "${FILESDIR}"/${P}-mayhem.patch + "${FILESDIR}"/${P}-set_proper_dir_permissions.patch + "${FILESDIR}"/${P}-cxx11.patch + "${FILESDIR}"/${P}-gcc7.patch +) src_prepare() { + default sed \ -e '/@/s:.*;:\t:g' \ -e '/Linking/s:$(CC):$(CC) $(CFLAGS) $(LDFLAGS):g' \ -i t_coffee_source/makefile || die - epatch \ - "${FILESDIR}"/${P}-mayhem.patch \ - "${FILESDIR}"/${P}-set_proper_dir_permissions.patch } src_compile() { - [[ $(gcc-version) == "3.4" ]] || \ - [[ $(gcc-version) == "4.1" ]] && \ - append-flags -fno-unit-at-a-time emake \ V=1 \ CC="$(tc-getCXX)" \ @@ -49,8 +49,6 @@ src_compile() { src_install() { dobin t_coffee_source/t_coffee - if use examples; then - insinto /usr/share/${PN} - doins -r example - fi + insinto /usr/share/${PN} + doins -r example } diff --git a/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild b/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild deleted file mode 100644 index 9f32c135fb78..000000000000 --- a/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils flag-o-matic fortran-2 toolchain-funcs versionator - -MY_PV="$(replace_version_separator 2 .r)" -MY_P="T-COFFEE_distribution_Version_${MY_PV}" - -DESCRIPTION="A multiple sequence alignment package" -HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html" -SRC_URI="http://www.tcoffee.org/Packages/Stable/Version_${MY_PV}/${MY_P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="amd64 ppc ~ppc64 x86 ~amd64-linux ~x86-linux" -IUSE="examples" - -RDEPEND=" - sci-biology/clustalw - sci-chemistry/tm-align" -DEPEND="" - -S="${WORKDIR}/${MY_P}" - -die_compile() { - echo - eerror "If you experience an internal compiler error (consult the above" - eerror "messages), try compiling t-coffee using very modest compiler flags." - eerror "See bug #114745 on the Gentoo Bugzilla for more details." - die "Compilation failed" -} - -src_prepare() { - epatch "${FILESDIR}"/${P}-flags.patch -} - -src_compile() { - [[ $(gcc-version) == "3.4" ]] || \ - [[ $(gcc-version) == "4.1" ]] && \ - append-flags -fno-unit-at-a-time - emake \ - CC="$(tc-getCC)" \ - CFLAGS="${CFLAGS}" \ - -C t_coffee_source t_coffee -} - -src_install() { - dobin t_coffee_source/t_coffee - - if use examples; then - insinto /usr/share/${PN} - doins -r example - fi -} |